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GeneBe

rs2306283

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM1PM2_SupportingBP4_Moderate

The NM_006446(SLCO1B1):c.388A>C(p.Asn130His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N130D) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

SLCO1B1
NM_006446 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.275

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM1
?
In a glycosylation_site N-linked (GlcNAc...) asparagine (size 0) in uniprot entity SO1B1_HUMAN
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.08858788).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO1B1NM_006446.5 linkuse as main transcriptc.388A>C p.Asn130His missense_variant 5/15 ENST00000256958.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO1B1ENST00000256958.3 linkuse as main transcriptc.388A>C p.Asn130His missense_variant 5/151 NM_006446.5 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000146
AC:
2
AN:
1372218
Hom.:
0
AF XY:
0.00000146
AC XY:
1
AN XY:
686026
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000194
Gnomad4 OTH exome
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.077
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.74
Cadd
Benign
4.2
Dann
Benign
0.84
DEOGEN2
Benign
0.051
T
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.027
N
LIST_S2
Benign
0.13
T
M_CAP
Benign
0.0058
T
MetaRNN
Benign
0.089
T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.3
M
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.26
T
PROVEAN
Uncertain
-2.9
D
REVEL
Benign
0.040
Sift
Benign
0.031
D
Sift4G
Benign
0.099
T
Polyphen
0.019
B
Vest4
0.14
MutPred
0.36
Gain of helix (P = 0.0496);
MVP
0.10
MPC
0.011
ClinPred
0.19
T
GERP RS
-2.6
Varity_R
0.084
gMVP
0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2306283; hg19: chr12-21329738;